메뉴 건너뛰기




Volumn 8, Issue 4, 1999, Pages 750-759

Factors limiting the performance of prediction-based fold recognition methods

Author keywords

Fold recognition; Protein function identification; Protein structure prediction; Remote homologues; Secondary structure and accessibility predictions; Sequence annotation; Threading

Indexed keywords

ARTICLE; GENOME; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STRUCTURE ACTIVITY RELATION;

EID: 0032942294     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.4.750     Document Type: Article
Times cited : (20)

References (41)
  • 1
    • 0032539805 scopus 로고    scopus 로고
    • Seeking an ancient enzyme in Methanococcus jannaschii using ORF, a program based on predicted secondary structure comparisons
    • Aurora R, Rose G. 1998. Seeking an ancient enzyme in Methanococcus jannaschii using ORF, a program based on predicted secondary structure comparisons. Proc Natl Acad Sci USA 95:2818-2823.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 2818-2823
    • Aurora, R.1    Rose, G.2
  • 3
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known 3-dimensional structure
    • Bowie JU, Luthy R, Eisenberg D. 1991. A method to identify protein sequences that fold into a known 3-dimensional structure. Science 253:164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 4
    • 0029974002 scopus 로고    scopus 로고
    • Evaluation of threading specificity and accuracy
    • Bryant SH. 1996. Evaluation of threading specificity and accuracy. Proteins Struct Fund Genet 26:172-185.
    • (1996) Proteins Struct Fund Genet , vol.26 , pp. 172-185
    • Bryant, S.H.1
  • 5
  • 6
    • 0027318317 scopus 로고
    • An empirical energy function for threading protein sequence through folding motif
    • Bryant SH, Lawrence CE. 1993. An empirical energy function for threading protein sequence through folding motif. Proteins Struct Fund Genet 5:92-112.
    • (1993) Proteins Struct Fund Genet , vol.5 , pp. 92-112
    • Bryant, S.H.1    Lawrence, C.E.2
  • 7
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins
    • Dayhoff M, ed. Silver Spring, Maryland: National Biomedical Research Foundation
    • Dayhoff M, Schwartz RM, Orcutt BC. 1978. A model of evolutionary change in proteins. In: Dayhoff M, ed. Atlas of protein sequence and structure, vol 5 (suppl 3). Silver Spring, Maryland: National Biomedical Research Foundation, pp 345-352.
    • (1978) Atlas of Protein Sequence and Structure , vol.5 , Issue.SUPPL. 3 , pp. 345-352
    • Dayhoff, M.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 8
    • 0025296915 scopus 로고
    • Alignment of protein sequences using secondary structure: A modified dynamic programming method
    • Fischel-Ghodsian F, Mathiowitz G, Smith T. 1990. Alignment of protein sequences using secondary structure: A modified dynamic programming method. Protein Eng 3:517-581.
    • (1990) Protein Eng , vol.3 , pp. 517-581
    • Fischel-Ghodsian, F.1    Mathiowitz, G.2    Smith, T.3
  • 9
    • 0029874551 scopus 로고    scopus 로고
    • Protein fold recognition using sequence-derived predictions
    • Fischer D, Eisenberg D. 1996. Protein fold recognition using sequence-derived predictions. Protein Sci 5:947-955.
    • (1996) Protein Sci , vol.5 , pp. 947-955
    • Fischer, D.1    Eisenberg, D.2
  • 11
    • 0029982530 scopus 로고    scopus 로고
    • The structural alignment between two proteins - Is there a unique answer?
    • Godzik A. 1996. The structural alignment between two proteins - Is there a unique answer? Protein Sci 5:1325-1338.
    • (1996) Protein Sci , vol.5 , pp. 1325-1338
    • Godzik, A.1
  • 12
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones DT, Taylor WR, Thornton JM. 1992. A new approach to protein fold recognition. Nature 358:86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 13
    • 0020997912 scopus 로고
    • A dictionary of protein secondary structure
    • Kabsch W, Sander C. 1983. A dictionary of protein secondary structure. Biopolymers 22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 14
    • 0028318094 scopus 로고
    • Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
    • Kocher J-P, Rooman MJ, Wodak SJ. 1994. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 235:1598-1613.
    • (1994) J Mol Biol , vol.235 , pp. 1598-1613
    • Kocher, J.-P.1    Rooman, M.J.2    Wodak, S.J.3
  • 15
    • 0029805706 scopus 로고    scopus 로고
    • The new genomics - Global views of biology
    • Lander ES. 1996. The new genomics - Global views of biology. Science 274:536-539.
    • (1996) Science , vol.274 , pp. 536-539
    • Lander, E.S.1
  • 16
    • 0028818340 scopus 로고
    • Protein structure prediction by threading methods: Evaluation of current techniques
    • Lemer CM-R, Rooman MJ, Wodak SJ. 1995. Protein structure prediction by threading methods: Evaluation of current techniques. Proteins Struct Funct Genet 25:337-355.
    • (1995) Proteins Struct Funct Genet , vol.25 , pp. 337-355
    • Lemer, C.M.-R.1    Rooman, M.J.2    Wodak, S.J.3
  • 17
    • 0030811206 scopus 로고    scopus 로고
    • A measure of success in fold recognition
    • Marchler-Bauer A, Bryant SH. 1997. A measure of success in fold recognition. TIBS 22:236-240.
    • (1997) TIBS , vol.22 , pp. 236-240
    • Marchler-Bauer, A.1    Bryant, S.H.2
  • 20
    • 0031762430 scopus 로고    scopus 로고
    • Sequences annotated by structure: A tool to facilitate the use of structural information sequence analysis
    • Milburn D, Laskowski R, Thornton JM. 1998. Sequences annotated by structure: A tool to facilitate the use of structural information sequence analysis. Protein Eng 11:855-859.
    • (1998) Protein Eng , vol.11 , pp. 855-859
    • Milburn, D.1    Laskowski, R.2    Thornton, J.M.3
  • 21
    • 0028961335 scopus 로고
    • SCOP - A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. SCOP - A structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 22
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequences of two proteins
    • Needleman SB, Wunsch CD. 1970. A general method applicable to the search for similarities in the amino acid sequences of two proteins. J Mol Biol 43:443-453.
    • (1970) J Mol Biol , vol.43 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 23
    • 0027302043 scopus 로고
    • Prediction of protein-structure by evaluation of sequence-structure fitness - Aligning sequences to contact profiles derived from 3D structures
    • Ouzounis C, Sander C, Scharf M, Schneider R. 1993. Prediction of protein-structure by evaluation of sequence-structure fitness - Aligning sequences to contact profiles derived from 3D structures. J Mol Biol 232:805-825.
    • (1993) J Mol Biol , vol.232 , pp. 805-825
    • Ouzounis, C.1    Sander, C.2    Scharf, M.3    Schneider, R.4
  • 24
    • 0031564630 scopus 로고    scopus 로고
    • A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence
    • Rice D, Eisenberg D. 1997. A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J Mol Biol 267:1026-1038.
    • (1997) J Mol Biol , vol.267 , pp. 1026-1038
    • Rice, D.1    Eisenberg, D.2
  • 25
    • 0031307341 scopus 로고    scopus 로고
    • Fold assignments for amino acid sequences of the CASP2 experiment
    • Rice D, Fischer D, Weiss R, Eisenberg D. 1997. Fold assignments for amino acid sequences of the CASP2 experiment. Proteins Struct Funct Genet (Suppl 1): 113-122.
    • (1997) Proteins Struct Funct Genet , Issue.SUPPL. 1 , pp. 113-122
    • Rice, D.1    Fischer, D.2    Weiss, R.3    Eisenberg, D.4
  • 27
    • 0027291015 scopus 로고
    • Prediction of secondary structure at better than 70% accuracy
    • Rost B, Sander C. 1993. Prediction of secondary structure at better than 70% accuracy. J Mol Biol 232:584-599.
    • (1993) J Mol Biol , vol.232 , pp. 584-599
    • Rost, B.1    Sander, C.2
  • 28
    • 0031577260 scopus 로고    scopus 로고
    • Protein fold recognition by prediction-based threading
    • Rost B, Schneider R, Sander C. 1997. Protein fold recognition by prediction-based threading. J Mol Biol 270:471-480.
    • (1997) J Mol Biol , vol.270 , pp. 471-480
    • Rost, B.1    Schneider, R.2    Sander, C.3
  • 29
    • 0026743174 scopus 로고
    • Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
    • Russell RB, Barton G. 1992. Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels. Proteins Struct Funct Genet 14:309-323.
    • (1992) Proteins Struct Funct Genet , vol.14 , pp. 309-323
    • Russell, R.B.1    Barton, G.2
  • 30
    • 0029951995 scopus 로고    scopus 로고
    • Protein fold recognition by mapping predicted secondary structures
    • Russell RB, Copley RR, Barton GJ. 1996. Protein fold recognition by mapping predicted secondary structures. J Mol Biol 259:349-365.
    • (1996) J Mol Biol , vol.259 , pp. 349-365
    • Russell, R.B.1    Copley, R.R.2    Barton, G.J.3
  • 31
    • 0031909873 scopus 로고    scopus 로고
    • Recognition of analogous and homologous protein folds - Assessment of prediction success and associated alignment accuracy using empirical substitution matrices
    • Russell RB, Saqi MAS, Bates P, Sayle RA, Stemberg MJE. 1998. Recognition of analogous and homologous protein folds - Assessment of prediction success and associated alignment accuracy using empirical substitution matrices. Protein Eng 11:1-9.
    • (1998) Protein Eng , vol.11 , pp. 1-9
    • Russell, R.B.1    Saqi, M.A.S.2    Bates, P.3    Sayle, R.A.4    Stemberg, M.J.E.5
  • 32
    • 0031566432 scopus 로고    scopus 로고
    • Recognition of analogous and homologous protein folds: Analysis of sequence and structure conservation
    • Russell RB, Saqi MAS, Sayle RA, Bates PA, Stemberg MJE. 1997. Recognition of analogous and homologous protein folds: Analysis of sequence and structure conservation. J Mol Biol 269:423-439.
    • (1997) J Mol Biol , vol.269 , pp. 423-439
    • Russell, R.B.1    Saqi, M.A.S.2    Sayle, R.A.3    Bates, P.A.4    Stemberg, M.J.E.5
  • 35
  • 36
    • 0026704815 scopus 로고
    • Detection of native-like models for amino-acid-sequences of unknown 3-dimensional structure in a data-base of known protein conformations
    • Sippl MJ, Weitckus S. 1992. Detection of native-like models for amino-acid-sequences of unknown 3-dimensional structure in a data-base of known protein conformations. Proteins Struct Funct Genet 13:258-271.
    • (1992) Proteins Struct Funct Genet , vol.13 , pp. 258-271
    • Sippl, M.J.1    Weitckus, S.2
  • 37
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith TF, Waterman MS. 1981. Identification of common molecular subsequences. J Mol Biol 147:195-197.
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 38
    • 0029147823 scopus 로고
    • Intrinsic φ,ψ propensities of amino acids, derived from the coil regions of known structures
    • Swindells MB, MacArthur MW, Thornton JM. 1995. Intrinsic φ,ψ propensities of amino acids, derived from the coil regions of known structures. Nature Struct Biol 2:596-603.
    • (1995) Nature Struct Biol , vol.2 , pp. 596-603
    • Swindells, M.B.1    MacArthur, M.W.2    Thornton, J.M.3
  • 39
    • 0024349252 scopus 로고
    • Protein structure alignment
    • Taylor WR, Orengo CA. 1989. Protein structure alignment. J Mol Biol 208: 1-22.
    • (1989) J Mol Biol , vol.208 , pp. 1-22
    • Taylor, W.R.1    Orengo, C.A.2
  • 40
  • 41
    • 0030334647 scopus 로고    scopus 로고
    • Optimum superimposition of protein structures: Ambiguities and implications
    • Zu-Kang F, Sippl MJ. 1996. Optimum superimposition of protein structures: Ambiguities and implications. Folding Design 1:123-132.
    • (1996) Folding Design , vol.1 , pp. 123-132
    • Zu-Kang, F.1    Sippl, M.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.